Multiple sequence alignment - TraesCS4B01G117600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G117600 chr4B 100.000 6069 0 0 1 6069 136526214 136532282 0.000000e+00 11208
1 TraesCS4B01G117600 chr4D 93.247 6145 218 63 1 6069 96517354 96523377 0.000000e+00 8866
2 TraesCS4B01G117600 chr4A 94.363 3938 148 34 2171 6069 482137616 482133714 0.000000e+00 5975
3 TraesCS4B01G117600 chr4A 90.444 2072 97 43 150 2175 482139676 482137660 0.000000e+00 2636
4 TraesCS4B01G117600 chr4A 91.558 154 10 2 2 152 482140085 482139932 6.160000e-50 209
5 TraesCS4B01G117600 chr5A 81.008 595 89 17 4194 4766 284694365 284694957 9.280000e-123 451
6 TraesCS4B01G117600 chr5A 80.942 467 54 22 983 1442 284691330 284691768 2.710000e-88 337
7 TraesCS4B01G117600 chr5A 79.556 450 68 16 3442 3885 284693573 284694004 3.560000e-77 300
8 TraesCS4B01G117600 chr5D 80.634 599 88 13 4194 4766 215877695 215878291 7.220000e-119 438
9 TraesCS4B01G117600 chr5D 80.851 470 51 24 983 1443 215874913 215875352 3.510000e-87 333
10 TraesCS4B01G117600 chr5D 79.677 433 66 15 3442 3868 215876901 215877317 5.950000e-75 292
11 TraesCS4B01G117600 chr5B 88.302 265 31 0 4194 4458 231731999 231732263 9.820000e-83 318
12 TraesCS4B01G117600 chr5B 79.744 469 59 23 983 1443 231729288 231729728 2.120000e-79 307
13 TraesCS4B01G117600 chr5B 80.139 433 64 15 3442 3868 231731204 231731620 2.750000e-78 303


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G117600 chr4B 136526214 136532282 6068 False 11208.000000 11208 100.000000 1 6069 1 chr4B.!!$F1 6068
1 TraesCS4B01G117600 chr4D 96517354 96523377 6023 False 8866.000000 8866 93.247000 1 6069 1 chr4D.!!$F1 6068
2 TraesCS4B01G117600 chr4A 482133714 482140085 6371 True 2940.000000 5975 92.121667 2 6069 3 chr4A.!!$R1 6067
3 TraesCS4B01G117600 chr5A 284691330 284694957 3627 False 362.666667 451 80.502000 983 4766 3 chr5A.!!$F1 3783
4 TraesCS4B01G117600 chr5D 215874913 215878291 3378 False 354.333333 438 80.387333 983 4766 3 chr5D.!!$F1 3783
5 TraesCS4B01G117600 chr5B 231729288 231732263 2975 False 309.333333 318 82.728333 983 4458 3 chr5B.!!$F1 3475

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
520 809 0.322008 CCAACTCCAACTCCAGCTCC 60.322 60.0 0.00 0.0 0.00 4.70 F
1107 1424 0.320771 CCCTGCGCTATTTAGCCGAT 60.321 55.0 9.73 0.0 46.34 4.18 F
2456 3463 0.036388 TTCTCATCCGGTGCAAGACC 60.036 55.0 0.00 0.0 42.07 3.85 F
3890 5033 0.821301 TGCCATTCCGTTGACAGCAA 60.821 50.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1664 0.107848 ATCCATGGAACCGGTCGAAC 60.108 55.000 20.67 0.0 0.00 3.95 R
2505 3512 1.269448 TGCGTTCAAAAGGAGAATGGC 59.731 47.619 0.00 0.0 33.62 4.40 R
4405 5581 2.088423 TGGGTCATATTTGGTGCGAAC 58.912 47.619 0.00 0.0 0.00 3.95 R
5586 6791 0.099436 ATTGCAATTTCTCTCGCGGC 59.901 50.000 5.99 0.0 0.00 6.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.489022 ACATTATGATCATGACTGTTGGATGG 59.511 38.462 18.72 0.00 0.00 3.51
27 28 4.146745 TGATCATGACTGTTGGATGGAG 57.853 45.455 0.00 0.00 0.00 3.86
50 51 7.166691 AGATCTAACGGCTAGAAAAAGTGTA 57.833 36.000 0.00 0.00 40.12 2.90
89 93 1.790623 CTTACACACGGTCGTTCCTTG 59.209 52.381 0.00 4.90 40.71 3.61
157 419 5.844914 CACGGAAATCTACGAAGTATAGTCG 59.155 44.000 4.58 4.58 44.56 4.18
174 436 1.602377 GTCGTAAAAGTGCTGCCAACT 59.398 47.619 0.00 0.00 0.00 3.16
191 453 4.332819 GCCAACTAAAAGCGATAGTCATGT 59.667 41.667 0.00 0.00 32.54 3.21
251 520 4.857037 TCAGTCGAATGAATCAAGTACACG 59.143 41.667 14.01 0.00 0.00 4.49
265 534 7.744087 TCAAGTACACGAGGTAGTTAGTTAA 57.256 36.000 10.29 0.00 42.42 2.01
268 537 9.415544 CAAGTACACGAGGTAGTTAGTTAATTT 57.584 33.333 10.29 0.00 42.42 1.82
269 538 8.976986 AGTACACGAGGTAGTTAGTTAATTTG 57.023 34.615 0.00 0.00 31.42 2.32
270 539 6.716898 ACACGAGGTAGTTAGTTAATTTGC 57.283 37.500 0.00 0.00 0.00 3.68
297 578 3.492383 CACATCACATCATTACTCTCGGC 59.508 47.826 0.00 0.00 0.00 5.54
309 590 6.701841 TCATTACTCTCGGCTTAATTTAGCTG 59.298 38.462 17.31 17.31 46.66 4.24
402 685 4.368808 CACCGCACGCGTGAAAGG 62.369 66.667 41.19 35.94 37.81 3.11
510 799 3.874383 TCAATCCAACTCCAACTCCAA 57.126 42.857 0.00 0.00 0.00 3.53
515 804 1.142870 CCAACTCCAACTCCAACTCCA 59.857 52.381 0.00 0.00 0.00 3.86
516 805 2.498167 CAACTCCAACTCCAACTCCAG 58.502 52.381 0.00 0.00 0.00 3.86
517 806 0.398318 ACTCCAACTCCAACTCCAGC 59.602 55.000 0.00 0.00 0.00 4.85
518 807 0.689623 CTCCAACTCCAACTCCAGCT 59.310 55.000 0.00 0.00 0.00 4.24
519 808 0.687354 TCCAACTCCAACTCCAGCTC 59.313 55.000 0.00 0.00 0.00 4.09
520 809 0.322008 CCAACTCCAACTCCAGCTCC 60.322 60.000 0.00 0.00 0.00 4.70
521 810 0.397941 CAACTCCAACTCCAGCTCCA 59.602 55.000 0.00 0.00 0.00 3.86
522 811 0.398318 AACTCCAACTCCAGCTCCAC 59.602 55.000 0.00 0.00 0.00 4.02
523 812 1.298014 CTCCAACTCCAGCTCCACC 59.702 63.158 0.00 0.00 0.00 4.61
524 813 1.152030 TCCAACTCCAGCTCCACCT 60.152 57.895 0.00 0.00 0.00 4.00
525 814 1.194781 TCCAACTCCAGCTCCACCTC 61.195 60.000 0.00 0.00 0.00 3.85
526 815 1.298014 CAACTCCAGCTCCACCTCC 59.702 63.158 0.00 0.00 0.00 4.30
570 871 2.597217 CCCAACGCACCACCACAT 60.597 61.111 0.00 0.00 0.00 3.21
572 873 1.896183 CCAACGCACCACCACATCA 60.896 57.895 0.00 0.00 0.00 3.07
777 1078 3.377485 CACCAGAGCAGAAATCAATCCTG 59.623 47.826 0.00 0.00 0.00 3.86
861 1162 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
863 1164 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
896 1197 3.901222 GGAACAAGGAAGGAAATCCCAAA 59.099 43.478 0.00 0.00 40.59 3.28
897 1198 4.262463 GGAACAAGGAAGGAAATCCCAAAC 60.262 45.833 0.00 0.00 40.59 2.93
898 1199 3.239449 ACAAGGAAGGAAATCCCAAACC 58.761 45.455 0.00 0.00 40.59 3.27
899 1200 3.116746 ACAAGGAAGGAAATCCCAAACCT 60.117 43.478 0.00 0.00 40.59 3.50
900 1201 3.458044 AGGAAGGAAATCCCAAACCTC 57.542 47.619 0.00 0.00 40.59 3.85
1107 1424 0.320771 CCCTGCGCTATTTAGCCGAT 60.321 55.000 9.73 0.00 46.34 4.18
1194 1511 1.152735 CGGAGGATCGGAGGAGGAA 60.153 63.158 0.00 0.00 37.69 3.36
1480 1798 1.555075 TCCTTCATCAGCTGGTACACC 59.445 52.381 15.13 0.00 0.00 4.16
1548 1866 5.928264 TGCATATTCAGTATCATCCAGTTCG 59.072 40.000 0.00 0.00 0.00 3.95
1563 1881 4.990543 CAGTTCGCACTGTTATTTCTGA 57.009 40.909 7.07 0.00 44.96 3.27
1564 1882 5.342806 CAGTTCGCACTGTTATTTCTGAA 57.657 39.130 7.07 0.00 44.96 3.02
1565 1883 5.140177 CAGTTCGCACTGTTATTTCTGAAC 58.860 41.667 7.07 0.00 44.96 3.18
1566 1884 5.050091 CAGTTCGCACTGTTATTTCTGAACT 60.050 40.000 7.07 0.00 44.96 3.01
1600 1918 9.645059 TTTCACTTTTCAACATGTCAACATTTA 57.355 25.926 0.00 0.00 33.61 1.40
1621 2119 3.866651 AGATGCTAGTACTGTTTGCCTG 58.133 45.455 5.39 0.00 0.00 4.85
1646 2144 1.733912 GGTCGTGGTTTTAATCGGGAC 59.266 52.381 0.00 0.00 0.00 4.46
1649 2147 3.068560 TCGTGGTTTTAATCGGGACAAG 58.931 45.455 0.00 0.00 0.00 3.16
1659 2157 1.496060 TCGGGACAAGCAGATGGTAT 58.504 50.000 0.00 0.00 0.00 2.73
1669 2167 1.202452 GCAGATGGTATTTTGGCTGGC 60.202 52.381 0.00 0.00 0.00 4.85
1682 2182 1.368579 GCTGGCATTGCAACCTGTT 59.631 52.632 11.39 0.00 0.00 3.16
1704 2207 1.242076 CTTTGGTCTGAAGCTGGGTG 58.758 55.000 0.00 0.00 0.00 4.61
1710 2213 1.002868 CTGAAGCTGGGTGGACAGG 60.003 63.158 0.00 0.00 38.90 4.00
1782 2341 2.897846 CCAACGCACACAACCGGA 60.898 61.111 9.46 0.00 0.00 5.14
2105 3055 5.989777 ACACTTGCGTTGTAAGTAGAGAAAT 59.010 36.000 0.00 0.00 36.42 2.17
2113 3065 8.160976 GCGTTGTAAGTAGAGAAATTAACAGAC 58.839 37.037 0.00 0.00 0.00 3.51
2160 3115 2.033550 CCTCTACTAGTTACAGCAGCCG 59.966 54.545 0.00 0.00 0.00 5.52
2229 3232 5.871396 TGTAAGCAAACCCACCAAATAAA 57.129 34.783 0.00 0.00 0.00 1.40
2230 3233 6.426646 TGTAAGCAAACCCACCAAATAAAT 57.573 33.333 0.00 0.00 0.00 1.40
2266 3269 8.181573 CCAACATCCATGTGTTATAAAGTGTAC 58.818 37.037 1.72 0.00 40.17 2.90
2273 3276 8.332464 CCATGTGTTATAAAGTGTACGGTTATG 58.668 37.037 0.00 0.00 0.00 1.90
2275 3278 9.656040 ATGTGTTATAAAGTGTACGGTTATGAA 57.344 29.630 6.00 0.00 0.00 2.57
2306 3310 3.688185 GGGTTCCGAAAATCAGAAGGTAC 59.312 47.826 0.00 0.00 0.00 3.34
2344 3348 5.066375 GCACACTCATGCCATTATTAAGTCA 59.934 40.000 0.00 0.00 39.86 3.41
2365 3372 5.877012 GTCATAACTTCTTGGATCAGCTCAA 59.123 40.000 0.00 0.00 0.00 3.02
2405 3412 3.950397 TGTTTGGTAGGAGTGCTTATGG 58.050 45.455 0.00 0.00 0.00 2.74
2456 3463 0.036388 TTCTCATCCGGTGCAAGACC 60.036 55.000 0.00 0.00 42.07 3.85
2477 3484 2.315925 ACTCGATGGTGCCTGTATTG 57.684 50.000 0.00 0.00 0.00 1.90
2485 3492 1.097232 GTGCCTGTATTGCTGCATCA 58.903 50.000 1.84 2.93 35.96 3.07
2622 3629 6.730447 TGATTGACCTGGGAATATCAAGAAA 58.270 36.000 0.00 0.00 34.71 2.52
2863 3873 4.935885 AGAGCAGAAAGAATAAAGCACG 57.064 40.909 0.00 0.00 0.00 5.34
3281 4380 7.495055 GCATAACTTGGGAGAATTCATCAATT 58.505 34.615 8.44 1.09 34.70 2.32
3308 4407 7.044181 TCTTACAGACCATCTTAATTGCTGAG 58.956 38.462 0.00 0.00 0.00 3.35
3376 4487 3.009723 ACCGAAATATGCCAAGTGACTG 58.990 45.455 0.00 0.00 0.00 3.51
3395 4506 7.231722 AGTGACTGTGTGATCTTTACTTCTACT 59.768 37.037 0.00 0.00 0.00 2.57
3454 4565 3.052036 CCAGTTCATGTTTCCTTTTGCG 58.948 45.455 0.00 0.00 0.00 4.85
3455 4566 3.490761 CCAGTTCATGTTTCCTTTTGCGT 60.491 43.478 0.00 0.00 0.00 5.24
3561 4672 8.391991 ATGATTCCAGAGGAAACAGTGTTCCA 62.392 42.308 19.93 5.39 45.13 3.53
3611 4722 4.838423 TCTGTATGAACAAGGAGGTCTTCA 59.162 41.667 0.00 0.00 34.49 3.02
3621 4732 1.202428 GGAGGTCTTCAGGTATGACGC 60.202 57.143 0.00 0.00 34.35 5.19
3890 5033 0.821301 TGCCATTCCGTTGACAGCAA 60.821 50.000 0.00 0.00 0.00 3.91
4097 5268 7.775053 ATGTGGTGTTATTAACTGGTTTGAT 57.225 32.000 7.99 0.00 0.00 2.57
4161 5332 7.660112 TGCAAACAATACTCTTGATGACAAAT 58.340 30.769 0.00 0.00 35.49 2.32
4580 5782 4.279671 AGATGCTAATACAGAAGACCCTCG 59.720 45.833 0.00 0.00 0.00 4.63
4828 6030 4.047059 GTCCGGTCGAGCGTGGAA 62.047 66.667 32.11 14.21 31.04 3.53
5081 6283 2.045634 GGTAGAAACCCCGGTGGC 60.046 66.667 0.00 0.00 40.21 5.01
5205 6407 0.039618 TGTTTTGAGGCTCATCCCCC 59.960 55.000 19.50 5.70 34.51 5.40
5260 6462 6.873605 GCTTATGAGTAAATTTGTGGCCTTTT 59.126 34.615 3.32 0.00 0.00 2.27
5291 6493 5.761003 TGTTGTACATGCATTTCTTCACTG 58.239 37.500 0.00 0.00 0.00 3.66
5298 6500 1.471684 GCATTTCTTCACTGCCTGGAG 59.528 52.381 0.00 0.00 0.00 3.86
5299 6501 2.787994 CATTTCTTCACTGCCTGGAGT 58.212 47.619 0.00 0.00 0.00 3.85
5300 6502 2.260844 TTTCTTCACTGCCTGGAGTG 57.739 50.000 12.05 12.05 44.14 3.51
5351 6553 6.536941 GTGTTATTCTCATCCTGACCTTTCTC 59.463 42.308 0.00 0.00 0.00 2.87
5356 6558 5.333581 TCTCATCCTGACCTTTCTCAAGTA 58.666 41.667 0.00 0.00 0.00 2.24
5395 6597 2.178876 CTGTATGCACGGTGTCCCCA 62.179 60.000 10.24 0.00 0.00 4.96
5477 6679 5.008613 TCTGTCCCGAGATTTTCACAAAAAG 59.991 40.000 0.00 0.00 37.76 2.27
5521 6726 0.161024 CTTCGTTCCTTGTCGTTCGC 59.839 55.000 0.00 0.00 0.00 4.70
5586 6791 6.329838 TGAAATTGCTGAAACAAAAACTCG 57.670 33.333 0.00 0.00 32.27 4.18
5588 6793 2.202295 TGCTGAAACAAAAACTCGCC 57.798 45.000 0.00 0.00 0.00 5.54
5604 6809 1.501741 GCCGCGAGAGAAATTGCAA 59.498 52.632 8.23 0.00 0.00 4.08
5608 6813 1.466192 CGCGAGAGAAATTGCAATGCA 60.466 47.619 13.82 2.72 36.47 3.96
5611 6816 4.353737 GCGAGAGAAATTGCAATGCATTA 58.646 39.130 13.82 0.00 38.76 1.90
5614 6819 6.436261 CGAGAGAAATTGCAATGCATTATCT 58.564 36.000 15.78 15.78 38.76 1.98
5620 6825 8.910944 AGAAATTGCAATGCATTATCTTCTACT 58.089 29.630 13.82 3.59 38.76 2.57
5621 6826 8.867112 AAATTGCAATGCATTATCTTCTACTG 57.133 30.769 13.82 0.00 38.76 2.74
5622 6827 7.578310 ATTGCAATGCATTATCTTCTACTGT 57.422 32.000 12.09 0.00 38.76 3.55
5623 6828 8.681486 ATTGCAATGCATTATCTTCTACTGTA 57.319 30.769 12.09 0.00 38.76 2.74
5624 6829 7.482654 TGCAATGCATTATCTTCTACTGTAC 57.517 36.000 12.53 0.00 31.71 2.90
5802 7008 2.458610 GCGAATTCGACCCGTTCCC 61.459 63.158 31.01 6.31 43.02 3.97
5837 7043 3.507233 GCTGGAATTCATTCACCAACAGA 59.493 43.478 7.93 0.00 38.53 3.41
5841 7047 6.690530 TGGAATTCATTCACCAACAGAAATC 58.309 36.000 7.93 0.00 38.53 2.17
5941 7147 0.835276 TGCATCAGCTCTACCTGCAT 59.165 50.000 0.00 0.00 42.74 3.96
5951 7157 4.596643 AGCTCTACCTGCATATTTCCATCT 59.403 41.667 0.00 0.00 0.00 2.90
5953 7159 5.486526 CTCTACCTGCATATTTCCATCTCC 58.513 45.833 0.00 0.00 0.00 3.71
6016 7222 3.389741 GCAAGATGCACGTTTCCAG 57.610 52.632 0.00 0.00 44.26 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.133003 CCGTTAGATCTCCATCCAACAGT 59.867 47.826 0.00 0.00 31.94 3.55
25 26 6.100668 ACACTTTTTCTAGCCGTTAGATCTC 58.899 40.000 0.00 0.00 38.19 2.75
27 28 8.421673 AATACACTTTTTCTAGCCGTTAGATC 57.578 34.615 0.00 0.00 38.19 2.75
157 419 4.444388 GCTTTTAGTTGGCAGCACTTTTAC 59.556 41.667 3.63 0.00 32.17 2.01
174 436 6.954616 TTTCGAACATGACTATCGCTTTTA 57.045 33.333 0.00 0.00 36.56 1.52
191 453 0.680618 TACCGTGCTCCCTTTTCGAA 59.319 50.000 0.00 0.00 0.00 3.71
251 520 8.604890 GTGATGAGCAAATTAACTAACTACCTC 58.395 37.037 0.00 0.00 0.00 3.85
265 534 6.465439 AATGATGTGATGTGATGAGCAAAT 57.535 33.333 0.00 0.00 0.00 2.32
268 537 5.677567 AGTAATGATGTGATGTGATGAGCA 58.322 37.500 0.00 0.00 0.00 4.26
269 538 5.990386 AGAGTAATGATGTGATGTGATGAGC 59.010 40.000 0.00 0.00 0.00 4.26
270 539 6.362820 CGAGAGTAATGATGTGATGTGATGAG 59.637 42.308 0.00 0.00 0.00 2.90
297 578 6.254589 CCAAGAGAGACGACAGCTAAATTAAG 59.745 42.308 0.00 0.00 0.00 1.85
309 590 0.532573 TGCCATCCAAGAGAGACGAC 59.467 55.000 0.00 0.00 0.00 4.34
357 640 9.012161 GGTTCTTCTCTTCTTTCTACTACAGTA 57.988 37.037 0.00 0.00 0.00 2.74
359 642 7.024768 CGGTTCTTCTCTTCTTTCTACTACAG 58.975 42.308 0.00 0.00 0.00 2.74
360 643 6.569994 GCGGTTCTTCTCTTCTTTCTACTACA 60.570 42.308 0.00 0.00 0.00 2.74
400 683 2.112072 TTGGTCTCCTCCTCCTGCCT 62.112 60.000 0.00 0.00 0.00 4.75
402 685 1.621672 CCTTGGTCTCCTCCTCCTGC 61.622 65.000 0.00 0.00 0.00 4.85
403 686 0.041833 TCCTTGGTCTCCTCCTCCTG 59.958 60.000 0.00 0.00 0.00 3.86
404 687 1.022903 ATCCTTGGTCTCCTCCTCCT 58.977 55.000 0.00 0.00 0.00 3.69
405 688 1.127343 CATCCTTGGTCTCCTCCTCC 58.873 60.000 0.00 0.00 0.00 4.30
406 689 2.166907 TCATCCTTGGTCTCCTCCTC 57.833 55.000 0.00 0.00 0.00 3.71
474 763 2.610859 GAAGGGAGGGTCAGGCCA 60.611 66.667 5.01 0.00 39.65 5.36
510 799 1.915769 GTGGAGGTGGAGCTGGAGT 60.916 63.158 0.00 0.00 0.00 3.85
515 804 0.773644 ATTTGTGTGGAGGTGGAGCT 59.226 50.000 0.00 0.00 0.00 4.09
516 805 1.168714 GATTTGTGTGGAGGTGGAGC 58.831 55.000 0.00 0.00 0.00 4.70
517 806 1.352352 AGGATTTGTGTGGAGGTGGAG 59.648 52.381 0.00 0.00 0.00 3.86
518 807 1.444933 AGGATTTGTGTGGAGGTGGA 58.555 50.000 0.00 0.00 0.00 4.02
519 808 3.545703 GATAGGATTTGTGTGGAGGTGG 58.454 50.000 0.00 0.00 0.00 4.61
520 809 3.054434 TGGATAGGATTTGTGTGGAGGTG 60.054 47.826 0.00 0.00 0.00 4.00
521 810 3.054361 GTGGATAGGATTTGTGTGGAGGT 60.054 47.826 0.00 0.00 0.00 3.85
522 811 3.545703 GTGGATAGGATTTGTGTGGAGG 58.454 50.000 0.00 0.00 0.00 4.30
523 812 3.054434 TGGTGGATAGGATTTGTGTGGAG 60.054 47.826 0.00 0.00 0.00 3.86
524 813 2.916269 TGGTGGATAGGATTTGTGTGGA 59.084 45.455 0.00 0.00 0.00 4.02
525 814 3.364460 TGGTGGATAGGATTTGTGTGG 57.636 47.619 0.00 0.00 0.00 4.17
526 815 5.299279 GGTAATGGTGGATAGGATTTGTGTG 59.701 44.000 0.00 0.00 0.00 3.82
570 871 4.352595 TGTGATTAGGGAGGGTTTCTTTGA 59.647 41.667 0.00 0.00 0.00 2.69
572 873 4.601857 TCTGTGATTAGGGAGGGTTTCTTT 59.398 41.667 0.00 0.00 0.00 2.52
759 1060 6.262720 GCTAATTCAGGATTGATTTCTGCTCT 59.737 38.462 0.00 0.00 32.27 4.09
842 1143 4.596585 GGTGGTGGTGGTGGTGGG 62.597 72.222 0.00 0.00 0.00 4.61
861 1162 2.115266 GTTCCTGGGTGGTGGTGG 59.885 66.667 0.00 0.00 37.07 4.61
863 1164 1.536676 CTTGTTCCTGGGTGGTGGT 59.463 57.895 0.00 0.00 37.07 4.16
896 1197 2.677228 CCGATTTGGCCAGGAGGT 59.323 61.111 5.11 0.00 37.19 3.85
1063 1374 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1064 1375 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1065 1376 1.292941 TGGAGGAGGAGGAGGAGGAG 61.293 65.000 0.00 0.00 0.00 3.69
1066 1377 1.230650 TGGAGGAGGAGGAGGAGGA 60.231 63.158 0.00 0.00 0.00 3.71
1067 1378 1.075600 GTGGAGGAGGAGGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
1068 1379 1.075600 GGTGGAGGAGGAGGAGGAG 60.076 68.421 0.00 0.00 0.00 3.69
1182 1499 0.187361 CCTCCTCTTCCTCCTCCGAT 59.813 60.000 0.00 0.00 0.00 4.18
1184 1501 0.467290 CTCCTCCTCTTCCTCCTCCG 60.467 65.000 0.00 0.00 0.00 4.63
1186 1503 0.930726 TCCTCCTCCTCTTCCTCCTC 59.069 60.000 0.00 0.00 0.00 3.71
1194 1511 2.600731 CGCTCCTCCTCCTCCTCT 59.399 66.667 0.00 0.00 0.00 3.69
1347 1664 0.107848 ATCCATGGAACCGGTCGAAC 60.108 55.000 20.67 0.00 0.00 3.95
1354 1671 0.532862 CCGAGGAATCCATGGAACCG 60.533 60.000 20.67 16.32 32.72 4.44
1480 1798 1.342174 ACAAGCATGTTTTGGGAGCTG 59.658 47.619 14.02 0.00 35.91 4.24
1508 1826 9.199982 CTGAATATGCAGAAACATTTTGAGTTT 57.800 29.630 4.46 0.00 41.53 2.66
1548 1866 8.535690 ACTACTTAGTTCAGAAATAACAGTGC 57.464 34.615 10.17 0.00 31.13 4.40
1566 1884 9.997482 GACATGTTGAAAAGTGAAAACTACTTA 57.003 29.630 0.00 0.00 37.39 2.24
1590 1908 8.480643 AACAGTACTAGCATCTAAATGTTGAC 57.519 34.615 0.00 0.00 35.18 3.18
1600 1918 3.261897 ACAGGCAAACAGTACTAGCATCT 59.738 43.478 0.00 0.00 0.00 2.90
1621 2119 3.976306 CCGATTAAAACCACGACCAAAAC 59.024 43.478 0.00 0.00 0.00 2.43
1646 2144 3.429822 CCAGCCAAAATACCATCTGCTTG 60.430 47.826 0.00 0.00 0.00 4.01
1649 2147 1.202452 GCCAGCCAAAATACCATCTGC 60.202 52.381 0.00 0.00 0.00 4.26
1659 2157 0.534652 GGTTGCAATGCCAGCCAAAA 60.535 50.000 0.59 0.00 36.27 2.44
1700 2203 2.041216 ACCTGAATTTACCTGTCCACCC 59.959 50.000 0.00 0.00 0.00 4.61
1704 2207 3.713826 TCCACCTGAATTTACCTGTCC 57.286 47.619 0.00 0.00 0.00 4.02
1782 2341 2.456073 AGTCTACGGAGGCACCTAAT 57.544 50.000 0.04 0.00 36.31 1.73
2299 3303 6.071728 TGTGCCAACTAAGTACTAGTACCTTC 60.072 42.308 25.97 4.89 40.14 3.46
2306 3310 5.386958 TGAGTGTGCCAACTAAGTACTAG 57.613 43.478 0.00 0.00 0.00 2.57
2337 3341 7.624549 AGCTGATCCAAGAAGTTATGACTTAA 58.375 34.615 2.38 0.00 45.88 1.85
2341 3345 5.423015 TGAGCTGATCCAAGAAGTTATGAC 58.577 41.667 0.00 0.00 0.00 3.06
2344 3348 6.059787 AGTTGAGCTGATCCAAGAAGTTAT 57.940 37.500 0.00 0.00 0.00 1.89
2365 3372 4.357918 ACAAAGCAAGAGGTGATACAGT 57.642 40.909 0.00 0.00 0.00 3.55
2373 3380 3.117663 TCCTACCAAACAAAGCAAGAGGT 60.118 43.478 0.00 0.00 0.00 3.85
2428 3435 4.102524 TGCACCGGATGAGAAATACCTTAT 59.897 41.667 9.46 0.00 0.00 1.73
2439 3446 4.208632 GGTCTTGCACCGGATGAG 57.791 61.111 9.46 0.00 34.56 2.90
2456 3463 3.384668 CAATACAGGCACCATCGAGTAG 58.615 50.000 0.00 0.00 0.00 2.57
2477 3484 1.303309 ATAAAGAGCGGTGATGCAGC 58.697 50.000 0.00 0.00 38.60 5.25
2503 3510 2.747446 GCGTTCAAAAGGAGAATGGCTA 59.253 45.455 0.00 0.00 33.62 3.93
2504 3511 1.541588 GCGTTCAAAAGGAGAATGGCT 59.458 47.619 0.00 0.00 33.62 4.75
2505 3512 1.269448 TGCGTTCAAAAGGAGAATGGC 59.731 47.619 0.00 0.00 33.62 4.40
2510 3517 2.325583 ACTGTGCGTTCAAAAGGAGA 57.674 45.000 0.00 0.00 0.00 3.71
2544 3551 1.819632 GGGGTCATTAGCGTGCCAG 60.820 63.158 0.00 0.00 0.00 4.85
2856 3866 5.987347 ACAATATAATACCTACGCGTGCTTT 59.013 36.000 24.59 10.64 0.00 3.51
2859 3869 8.792831 ATATACAATATAATACCTACGCGTGC 57.207 34.615 24.59 0.00 0.00 5.34
2950 3960 3.515502 TCCATCCTTGTACAGAGAACCAG 59.484 47.826 0.00 0.00 0.00 4.00
3092 4125 4.464008 TCTTTGCACATCCAGAAGTTTCT 58.536 39.130 0.00 0.00 38.25 2.52
3308 4407 5.136105 AGGCATCTTTTGAAGGACCATATC 58.864 41.667 0.00 0.00 0.00 1.63
3376 4487 9.141400 CCTTACAAGTAGAAGTAAAGATCACAC 57.859 37.037 0.00 0.00 30.57 3.82
3395 4506 8.630054 ACAATGCTCTAAAATACACCTTACAA 57.370 30.769 0.00 0.00 0.00 2.41
3454 4565 4.036734 TGAATCAGCTGAAGAACACCAAAC 59.963 41.667 22.50 2.34 0.00 2.93
3455 4566 4.206375 TGAATCAGCTGAAGAACACCAAA 58.794 39.130 22.50 0.00 0.00 3.28
3561 4672 5.645067 TCTTTGCATCATCAAGAGAATCGTT 59.355 36.000 0.00 0.00 42.67 3.85
3611 4722 6.995511 TTAAAATGCTAAAGCGTCATACCT 57.004 33.333 0.00 0.00 45.83 3.08
3915 5058 6.153067 AGAATCCGTCTATTGAAGATAAGCG 58.847 40.000 0.00 0.00 36.36 4.68
3931 5074 5.047306 TGACAAGTGTTGAGATAGAATCCGT 60.047 40.000 0.00 0.00 0.00 4.69
4097 5268 4.832266 ACTCAAGGACATAAAATTGTGGCA 59.168 37.500 0.00 0.00 0.00 4.92
4405 5581 2.088423 TGGGTCATATTTGGTGCGAAC 58.912 47.619 0.00 0.00 0.00 3.95
4580 5782 5.243730 CCAGATTGGACTCTTCTCTATCCTC 59.756 48.000 0.00 0.00 40.96 3.71
4784 5986 4.081087 ACTTGTATGGACAACGGAAGCTAT 60.081 41.667 0.00 0.00 40.72 2.97
5080 6282 1.280066 CACAACAACAAAGGCAGTGC 58.720 50.000 6.55 6.55 0.00 4.40
5081 6283 2.652941 ACACAACAACAAAGGCAGTG 57.347 45.000 0.00 0.00 0.00 3.66
5205 6407 3.933861 ATAAGTTAGTGAAGGCAGGGG 57.066 47.619 0.00 0.00 0.00 4.79
5260 6462 6.265196 AGAAATGCATGTACAACAAAGGAAGA 59.735 34.615 0.00 0.00 0.00 2.87
5291 6493 0.402121 AGAAACTTCCCACTCCAGGC 59.598 55.000 0.00 0.00 0.00 4.85
5298 6500 1.509703 GACGTCCAGAAACTTCCCAC 58.490 55.000 3.51 0.00 0.00 4.61
5299 6501 0.395312 GGACGTCCAGAAACTTCCCA 59.605 55.000 29.75 0.00 32.77 4.37
5300 6502 0.685660 AGGACGTCCAGAAACTTCCC 59.314 55.000 35.00 5.32 38.11 3.97
5351 6553 4.021102 ACCATGGTTGAGACCTTACTTG 57.979 45.455 13.00 0.00 46.66 3.16
5356 6558 2.578021 AGCATACCATGGTTGAGACCTT 59.422 45.455 25.38 0.00 46.66 3.50
5395 6597 6.368243 CAGAATAAAGCTATCTGATGCGATGT 59.632 38.462 11.32 0.00 0.00 3.06
5477 6679 9.727859 AGGAGAAAAGGTTAGAATAACTTCTTC 57.272 33.333 0.18 1.51 41.91 2.87
5521 6726 2.698855 AGAGTTGATGGTGGATTCGG 57.301 50.000 0.00 0.00 0.00 4.30
5586 6791 0.099436 ATTGCAATTTCTCTCGCGGC 59.901 50.000 5.99 0.00 0.00 6.53
5588 6793 1.186030 GCATTGCAATTTCTCTCGCG 58.814 50.000 9.83 0.00 0.00 5.87
5596 6801 8.472413 ACAGTAGAAGATAATGCATTGCAATTT 58.528 29.630 22.27 9.01 43.62 1.82
5604 6809 7.453126 AGCTAGGTACAGTAGAAGATAATGCAT 59.547 37.037 0.00 0.00 0.00 3.96
5608 6813 9.649316 AGAAAGCTAGGTACAGTAGAAGATAAT 57.351 33.333 0.00 0.00 0.00 1.28
5611 6816 6.183360 GCAGAAAGCTAGGTACAGTAGAAGAT 60.183 42.308 0.00 0.00 41.15 2.40
5614 6819 4.159879 GGCAGAAAGCTAGGTACAGTAGAA 59.840 45.833 0.00 0.00 44.79 2.10
5620 6825 2.257207 ACAGGCAGAAAGCTAGGTACA 58.743 47.619 0.00 0.00 44.79 2.90
5621 6826 3.263261 GAACAGGCAGAAAGCTAGGTAC 58.737 50.000 0.00 0.00 44.79 3.34
5622 6827 2.903784 TGAACAGGCAGAAAGCTAGGTA 59.096 45.455 0.00 0.00 44.79 3.08
5623 6828 1.699634 TGAACAGGCAGAAAGCTAGGT 59.300 47.619 0.00 0.00 44.79 3.08
5624 6829 2.354259 CTGAACAGGCAGAAAGCTAGG 58.646 52.381 0.00 0.00 44.79 3.02
5817 7023 6.295236 GGATTTCTGTTGGTGAATGAATTCCA 60.295 38.462 2.27 0.00 37.25 3.53
5837 7043 6.096846 CCGAATTTCTGATAAGGTTGGGATTT 59.903 38.462 0.00 0.00 0.00 2.17
5841 7047 4.096382 CACCGAATTTCTGATAAGGTTGGG 59.904 45.833 0.00 0.00 0.00 4.12
5875 7081 4.925054 CGCACAAATTTGATGGTGATCTTT 59.075 37.500 24.64 0.00 33.16 2.52
5927 7133 4.077300 TGGAAATATGCAGGTAGAGCTG 57.923 45.455 4.34 4.34 0.00 4.24
5941 7147 5.044919 ACAACATGTCAGGGAGATGGAAATA 60.045 40.000 0.00 0.00 37.59 1.40
5951 7157 0.250858 CCTGCACAACATGTCAGGGA 60.251 55.000 19.10 4.48 39.65 4.20
5953 7159 1.582968 GCCTGCACAACATGTCAGG 59.417 57.895 21.46 21.46 42.87 3.86
6009 7215 2.623416 CAACTTGGGAGGAACTGGAAAC 59.377 50.000 0.00 0.00 41.55 2.78
6016 7222 2.427506 CTACTGCAACTTGGGAGGAAC 58.572 52.381 0.00 0.00 0.00 3.62


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.